This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Past research has already tied our gut microbiome to many diseases. However, most research to date has focused on the large intestine, as collecting stool samples is less invasive than sampling the small intestine. Recently, researchers used standard-of-care endoscopies as an opportunity to collect samples from the first section of the small intestine, the duodenum. Using quantitative sequencing, they evaluated the patients' microbial loads. They found preliminary evidence of microbes traveling from the mouth to the small intestine, as 89% of the microbial taxa found in duodenum samples were also present in saliva samples from the same patient. Within the duodenum, the researchers identified a collection of bacterial taxa that, when present, often dominated the microbial population. These ‘disruptor taxa’ appeared to replace the strict anaerobes common in the duodenum and were more prevalent in individuals with the serious GI disorder small intestinal bacterial overgrowth (SIBO)..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Background Many journals now require authors share their data with other investigators, either by depositing the data in a public repository or making it freely available upon request. These policies are explicit, but remain largely untested. We sought to determine how well authors comply with such policies by requesting data from authors who had published in one of two journals with clear data sharing policies. Methods and Findings We requested data from ten investigators who had published in either PLoS Medicine or PLoS Clinical Trials. All responses were carefully documented. In the event that we were refused data, we reminded authors of the journal's data sharing guidelines. If we did not receive a response to our initial request, a second request was made. Following the ten requests for raw data, three investigators did not respond, four authors responded and refused to share their data, two email addresses were no longer valid, and one author requested further details. A reminder of PLoS's explicit requirement that authors share data did not change the reply from the four authors who initially refused. Only one author sent an original data set. Conclusions We received only one of ten raw data sets requested. This suggests that journal policies requiring data sharing do not lead to authors making their data sets available to independent investigators.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Our microbiome has profound impacts on our health, and technological advances have allowed for ever-growing pools of data from microbiome-wide studies. This means that our microbiome could be used to estimate disease risk, but the nature of the data makes the endeavor difficult. Similar issues with using genetics to predict disease risk led to the development of the polygenic risk score. Motivated by the success of that framework, a team of researchers recently developed the microbial risk score (MRS). MRS summarizes the complex microbial profile by first identifying a sub- community consisting of disease-associated microbial taxa and then integrating those microbial taxa into a continuous score based on the alpha diversity of the identified sub-community. MRS can be easily integrated with the other risk scores built upon metatranscriptomics, host genetics, or host transcriptomics, making it useful for 'multi-omics' approaches as well..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

TED Studies, created in collaboration with Wiley, are curated video collections — supplemented by rich educational materials — for students, educators and self-guided learners. in What Makes Us Human?, TED speakers tackle humanity’s oldest and deepest questions by playing with primates, excavating ancient remains, and DNA-mapping family trees. Explore how the next chapters of our own evolutionary story will be written thanks to new technologies that trace our origin. 

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Advancements in metagenomic technology have been a boon to research but may encroach on people’s expectation of privacy. A staggering amount of information can be derived from the cells we leave behind on everyday surfaces, and our ability to interpret this information to learn about YOU will only grow with time. While these advancements are not likely to ever be 100% accurate, they present a potential avenue for discrimination. Genetic privacy is not a new concept, and in the US and elsewhere, there are laws protecting people from some discrimination based on genomic-derived data, but metagenomics is not covered by the existing laws and requires its own ethical and legal scrutiny. Our world is rapidly becoming one with ubiquitous genetic, molecular, and data profiling. In that world, privacy will be difficult to protect unless statutes and laws are brought up to date with the advancement in biotechnology..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This course reviews the key genomic technologies and computational approaches that are driving advances in prognostics, diagnostics, and treatment. Throughout the semester, emphasis will return to issues surrounding the context of genomics in medicine including: what does a physician need to know? what sorts of questions will s/he likely encounter from patients? how should s/he respond? Lecturers will guide the student through real world patient-doctor interactions. Outcome considerations and socioeconomic implications of personalized medicine are also discussed. The first part of the course introduces key basic concepts of molecular biology, computational biology, and genomics. Continuing in the informatics applications portion of the course, lecturers begin each lecture block with a scenario, in order to set the stage and engage the student by showing: why is this important to know? how will the information presented be brought to bear on medical practice? The final section presents the ethical, legal, and social issues surrounding genomic medicine. A vision of how genomic medicine relates to preventative care and public health is presented in a discussion forum with the students where the following questions are explored: what is your level of preparedness now? what challenges must be met by the healthcare industry to get to where it needs to be?

Lecturers
Dr. Atul J. Butte
Dr. Steven A. Greenberg
Dr. Alvin Thong-Juak Kho
Dr. Peter Park
Dr. Marco F. Ramoni
Dr. Alberto A. Riva
Dr. Zoltan Szallasi
Dr. Jeffrey Mark Drazen
Dr. Todd Golub
Dr. Joel Hirschhorn
Dr. Greg Tucker-Kellogg
Dr. Scott Weiss

This course will focus on understanding aspects of modern technology displaying exponential growth curves and the impact on global quality of life through a weekly updated class project integrating knowledge and providing practical tools for political and business decision-making concerning new aspects of bioengineering, personalized medicine, genetically modified organisms, and stem cells. Interplays of economic, ethical, ecological, and biophysical modeling will be explored through multi-disciplinary teams of students, and individual brief reports.

Workshop overview for the Data Carpentry genomics curriculum. Data Carpentry’s aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. This workshop teaches data management and analysis for genomics research including: best practices for organization of bioinformatics projects and data, use of command-line utilities, use of command-line tools to analyze sequence quality and perform variant calling, and connecting to and using cloud computing. This workshop is designed to be taught over two full days of instruction. Please note that workshop materials for working with Genomics data in R are in “alpha” development. These lessons are available for review and for informal teaching experiences, but are not yet part of The Carpentries’ official lesson offerings. Interested in teaching these materials? We have an onboarding video and accompanying slides available to prepare Instructors to teach these lessons. After watching this video, please contact team@carpentries.org so that we can record your status as an onboarded Instructor. Instructors who have completed onboarding will be given priority status for teaching at centrally-organized Data Carpentry Genomics workshops.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Multidrug-resistant bacteria are a threat to both human and animal health worldwide. Bacteria often gain resistance to drugs by collecting antibiotic resistance genes (ARGs) from other bacteria. One potential hotbed for this exchange is wastewater treatment plants (WWTPs), where environmental bacteria co-mingle with human/animal-associated bacteria. Unfortunately, little is known about the epidemiology of multidrug-resistant bacteria in WWTPs. To close this gap, researchers isolated 82 multidrug-resistant bacterial strains from WWTPs and compared their genomes to bacterial genomes found in public databases. Most multidrug-resistant bacteria were not closely related to human/animal-associated bacteria, and those that were closely related had distinct plasmid profiles compared to relatives. Plasmids, as opposed to chromosomes, were also the main carriers of ARGs..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Genomics research has greatly increased understanding of the human gut microbiome, but the existing reference databases remain insufficient, failing to map up to half of the sequences obtained in human gut studies. To solve this problem, researchers recently created HumGut, a comprehensive global reference database for the genomes of gut microbes in healthy humans. The researchers built the database by comparing nearly half a million publicly available prokaryote genomes with over 3,500 gut metagenomes from healthy humans worldwide, and retaining the prokaryote genomes that closely matched the sequences in healthy human guts. HumGut was approximately the same size as the recently released UHGG collection and half the size of a standard reference database. However, HumGut outperformed both other databases in classifying metagenomic reads from human gut samples, resulting in a lower percentage of unclassified reads..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Most genetic studies of Alzheimer’s disease compare patient DNA to controls to identify mutations that increase disease risk. That approach has identified some risk variants, but none have led to effective treatments, and most of the genetic contributors are still unknown. Now, a team of researchers is tackling the problem from the opposite side, asking why some high-risk elderly people don’t have Alzheimer’s – a strategy that has discovered a protective mutation in a gene that may be a good drug target. To find protective mutations for Alzheimer’s, the scientists first searched the Utah Population Database for families with above-average rates of Alzheimer's that also had at least four people who were resilient to the disease -- that is, they were cognitively normal, despite being 75 years old or older, and having the APOE e4 allele, which increases risk more than 5-fold per copy..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers the structure and regulation of genes, as well as, the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into multicellular systems and organisms. In addition, each version of the subject has its own distinctive material.
7.012 focuses on the exploration of current research in cell biology, immunology, neurobiology, genomics, and molecular medicine.
Acknowledgments
The study materials, problem sets, and quiz materials used during Fall 2004 for 7.012 include contributions from past instructors, teaching assistants, and other members of the MIT Biology Department affiliated with course #7.012. Since the following works have evolved over a period of many years, no single source can be attributed.

The MIT Biology Department core Introductory Biology courses, 7.012, 7.013, 7.014, 7.015, and 7.016 all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. The focus of 7.013 is on genomic approaches to human biology, including neuroscience, development, immunology, tissue repair and stem cells, tissue engineering, and infectious and inherited diseases, including cancer.

The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers the structure and regulation of genes, as well as, the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into multicellular systems and organisms. In addition, each version of the subject has its own distinctive material.
7.014 focuses on the application of these fundamental principles, toward an understanding of microorganisms as geochemical agents responsible for the evolution and renewal of the biosphere and of their role in human health and disease.
Acknowledgements
The study materials, problem sets, and quiz materials used during Spring 2005 for 7.014 include contributions from past instructors, teaching assistants, and other members of the MIT Biology Department affiliated with course 7.014. Since the following works have evolved over a period of many years, no single source can be attributed.

The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. 7.013 focuses on the application of the fundamental principles toward an understanding of human biology. Topics include genetics, cell biology, molecular biology, disease (infectious agents, inherited diseases and cancer), developmental biology, neurobiology and evolution.
Biological function at the molecular level is particularly emphasized in all courses and covers the structure and regulation of genes, as well as, the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into multicellular systems and organisms. In addition, each version of the subject has its own distinctive material.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Microorganisms are critical drivers of biogeochemical cycles and are the most abundant organisms in frigid regions. Identifying the genomic traits of cold-loving microbes may help explain their physiology and adaptation, but recognizing which genomic traits are important for environmental adaptation is challenging. A new study compared the genomes of Arthrobacter bacteria isolated from the Tibetan Plateau with published genomes of related bacteria and defined a new group of Arthrobacter that live in polar and alpine environments. In the laboratory, the bacteria in this group grew comparatively rapidly at 0 °C. Compared to bacteria from warmer environments, the polar/alpine bacteria had different genomic and amino acid compositions, and their predicted proteins had different stability levels and functions..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Advances in genomic laboratory and bioinformatics techniques have allowed us to infer microbial ecology information from genomes. This ability has led to great advances in microbiome science; however, there is not yet a standard comprehensive workflow for functional annotation. Some software tools annotate metabolic functions, but the new tool 'METABOLIC' improves upon this and expands into biogeochemical pathways like the carbon cycle. METABOLIC takes sequence inputs from isolates, metagenome-assembled genomes, or single-cell genomes. The data can be processed through two workflow scales: genome and/or community. The genome-scale workflow annotates the genomes and validates motifs of conserved protein residues. It also analyzes metabolic pathways and calculates the microbial contributions to individual biogeochemical processes and cycles. The community-scale workflow adds to this by first determining the genome abundance in the microbiome..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

TED Studies, created in collaboration with Wiley, are curated video collections — supplemented by rich educational materials — for students, educators and self-guided learners. In The Deep Ocean, aquatic explorers take the TED stage to share what they've seen in the abyss of Earth's last frontier: the deep ocean, home to massive underwater mountains and valleys, giant smoking chimneys and an amazing array of animals.

This course provides an intensive introduction to artificial intelligence and its applications to problems of medical diagnosis, therapy selection, and monitoring and learning from databases. It meets with lectures and recitations of 6.034 Artificial Intelligence, whose material is supplemented by additional medical-specific readings in a weekly discussion session. Students are responsible for completing all homework assignments in 6.034 and for additional problems and/or papers.

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview:

"Metagenomics is a powerful technique for studying complex microbial communities. The key computational step in this method is clustering genomic sequences from mixed samples into potential microbial genomes, but accurately classifying sequences from complex metagenomes remains challenging. Some tools depend on k-mer frequency and coverage, but such methods struggle to distinguish between similar genomes. Methods that address the similar genomes problem, like ones that rely on single-copy marker genes, in turn struggle with complex datasets. The newly developed MetaDecoder balances these challenges by using both types of methods broken into two steps. First, MetaDecoder simplifies the dataset by generating preliminary groups of sequences with the Dirichlet Process Gaussian Mixture Model (DPGMM). Then, these preliminary clusters are clustered further with a k-mer frequency probabilistic model and a modified Gaussian Mixture Model of single-copy marker gene coverage..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.